Objective: China’s targeted poverty alleviation policy has a profound impact on the country’s rural economic and social development now. This study aimed to learn about the health status and health equity of rural poor residents under the implementation of the policy. It further explores the factors affecting the health status and health equity of rural poor residents in order to contribute to the improvement of the policy. Methods: The data of 1233 rural poor residents were collected from a questionnaire survey from 12 prefecture-level cities and areas of Shaanxi province in 2017, and the self-reported health was used to reflect the health status. A concentration index was applied to measure the inequity of the health status of rural poor residents. The decomposition method was employed to explore the source of health inequity. Results: The results showed that 44.56% of rural poor residents in Shaanxi province had a poor or very poor health status, which was affected by their economic level, gender, age, degree of education, and marital status. Additionally, participation in agricultural industry development, relocation, health poverty alleviation, and basic living standards were significantly correlated with health status. The concentration index of the health status of rural poor residents was 0.0327. The primary contributors to the health inequity in different regions varied, but the economic level and the degree of education were the most significant factors, and the targeted poverty alleviation policy had a significant impact on health equity. Conclusions: The results indicated that the health status of rural poor residents in Shaanxi province was generally poor, there was a pro-rich inequity in the health status, and the degree of education and economic level were the primary factors affecting the health status and health equity. The targeted poverty alleviation policy greatly impacted the health status and health equity of rural poor residents, and the difference in health status would lead to the inequity of benefits of the targeted poverty alleviation policy. In the future, the policy should focus on ensuring the sustainable development ability of rural residents with poor health status.